recipe bioconductor-splinetimer

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/splineTimeR.html

License:

GPL-3

Recipe:

/bioconductor-splinetimer/meta.yaml

Links:

biotools: splinetimer, doi: 10.1371/journal.pone.0160791

This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.

package bioconductor-splinetimer

(downloads) docker_bioconductor-splinetimer

versions:
1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0, 

1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-fis:

>=1.34.0,<1.35.0

depends bioconductor-gseabase:

>=1.68.0,<1.69.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends r-base:

>=4.4,<4.5.0a0

depends r-genenet:

>=1.2.13

depends r-gtools:

depends r-igraph:

depends r-longitudinal:

>=1.1.12

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-splinetimer

and update with::

   mamba update bioconductor-splinetimer

To create a new environment, run:

mamba create --name myenvname bioconductor-splinetimer

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-splinetimer:<tag>

(see `bioconductor-splinetimer/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-splinetimer/README.html)